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comparison COBRAxy/ras_to_bounds.py @ 120:567ffd4333d4 draft

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author luca_milaz
date Sun, 13 Oct 2024 16:44:58 +0000
parents 829ea241c3a1
children 7e1ce04cf192
comparison
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119:829ea241c3a1 120:567ffd4333d4
122 mediumRxns_ids (list of str): List of reaction IDs in the medium. Their RAS is set to zero, but they are already set in the model. 122 mediumRxns_ids (list of str): List of reaction IDs in the medium. Their RAS is set to zero, but they are already set in the model.
123 Returns: 123 Returns:
124 None 124 None
125 """ 125 """
126 for reaction in rxns_ids: 126 for reaction in rxns_ids:
127 if reaction in ras_row.index: #and reaction not in mediumRxns_ids 127 if reaction in ras_row.index and reaction not in mediumRxns_ids:
128 scaling_factor = ras_row[reaction] 128 scaling_factor = ras_row[reaction]
129 lower_bound=model.reactions.get_by_id(reaction).lower_bound 129 lower_bound=model.reactions.get_by_id(reaction).lower_bound
130 upper_bound=model.reactions.get_by_id(reaction).upper_bound 130 upper_bound=model.reactions.get_by_id(reaction).upper_bound
131 valMax=float((upper_bound)*scaling_factor) 131 valMax=float((upper_bound)*scaling_factor)
132 valMin=float((lower_bound)*scaling_factor) 132 valMin=float((lower_bound)*scaling_factor)
183 if(reaction == "EX_lac__L_e"): 183 if(reaction == "EX_lac__L_e"):
184 model.reactions.get_by_id(reaction).lower_bound = float(0.0) 184 model.reactions.get_by_id(reaction).lower_bound = float(0.0)
185 185
186 mediumRxns_ids = medium.keys() 186 mediumRxns_ids = medium.keys()
187 187
188 # Perform Flux Variability Analysis (FVA) 188 # Perform Flux Variability Analysis (FVA) on this medium
189 df_FVA = cobra.flux_analysis.flux_variability_analysis(model, fraction_of_optimum=0, processes=1).round(8) 189 df_FVA = cobra.flux_analysis.flux_variability_analysis(model, fraction_of_optimum=0, processes=1).round(8)
190 190
191 # Set FVA bounds 191 # Set FVA bounds
192 for reaction in rxns_ids: 192 for reaction in rxns_ids:
193 model.reactions.get_by_id(reaction).lower_bound = float(df_FVA.loc[reaction, "minimum"]) 193 model.reactions.get_by_id(reaction).lower_bound = float(df_FVA.loc[reaction, "minimum"])